Method and system using magnetic resonance imaging for tissue classification and bulk-density assignment

ABSTRACT

An apparatus includes a magnetic resonance imaging system, a processor for controlling the apparatus, and a memory containing machine executable instructions and a pulse sequence. The machine executable instructions and pulse sequence cause the processor to control the apparatus to: acquire magnetic resonance data from an imaging volume, wherein the magnetic resonance data includes gradient echo data; segment the magnetic resonance data into a plurality of segments, the segments including a fat segment, a water segment, a cortical bone segment, and an air segment; and create a bulk density map of the imaging volume from the segments.

CROSS-REFERENCES TO RELATED APPLICATIONS

This is a continuation-in-part patent application under 35 U.S.C. §120of U.S. patent application Ser. No. 14/126,979, filed on 17 Dec. 2013,which is a U.S. national stage application under 35 U.S.C. §371 ofInternational Application PCT/IB2012/053,050, filed on 18 Jun. 2012,which claims priority from European patent application 11171444.0, filedon 27 Jun. 2011, and U.S. Provisional Patent Application Ser. No.61/636,102, filed on 20 Apr. 2012. Priority to all of these patentapplications is claimed, and all of these patent applications are allhereby incorporated by reference in their entirety as if fully set forthherein.

TECHNICAL FIELD

The invention relates to magnetic resonance imaging, in particular tothe use of magnetic resonance imaging for radiation therapy planning

BACKGROUND AND SUMMARY

Magnetic Resonance (MR) images that can separate tissue, bone, and airare beneficial for all applications where MR is used in combination withirradiating imaging techniques, such as Positron Emission Tomography(PET) and Single Photon Emission Computed Tomography (SPECT), and withplanning for irradiating therapy techniques, such as MagneticResonance—Radio Therapy simulation. Unlike Hounsfield units used in CT,there is no simple relation between the MR image intensity and tissuedensity. For instance, using conventional MR sequences, cortical boneand air filled cavities both show no signal intensity whereas theirdensities are substantially different. Ultimately the ability toreliably identify additional tissue types in an MR image while theMR-acquisition time should be kept at a minimum would be beneficial.Additionally, the ability to reliably assign accurate electron densitiesto different voxels of an MR image would be beneficial for allowingcreation of a treatment dose plan based only on MR imaging, without theneed for registering MR images with separately generated CT images of animaging volume.

Embodiments of the invention may provide apparatus, systems, methods,and computer-readable storage medium for identifying different tissuetypes within a subject using magnetic resonance imaging. Embodiments mayachieve this by using a pulse sequence which can include commands toacquire free induction decay data and one or more gradient echoes. Thefree induction decay data is acquired at an echo time on a timescale ofmicroseconds. This enables the acquisition of free induction decay datafrom bone tissue. Data from one or more gradient echoes is alsoacquired. The commendation of acquiring the free induction decay dataand gradient echo data allows a variety of images to be constructed: anin-phase image, a fat-saturated image, a water-saturated image, and anultra-short echo time image. Using a pulse sequence which may be used toreconstruct such different images may be beneficial because all of theimage data necessary for radiation therapy dose planning and/orreconstructing images from radio-isotope imaging systems is provided.Using such a pulse sequence may also be beneficial because it may reducethe time necessary to acquire the images.

An embodiment of the invention may provide for a pulse sequence formagnetic resonance imaging which combines the features of an ultra-shortecho time (UTE) pulse sequence with one or more gradient echoes andDIXON reconstruction. For example the pulse sequence may be a UTEtriple-echo (UTILE) MR-sequence combining the UTE and DIXON acquisitionin a single acquisition. This example may be implemented using a pulsesequence that samples fast induced decay (FID) at short echo times, attime TE1, followed by two gradient echoes, at times TE2 and TE3. Theecho times TE2 and TE3 may be optionally adjusted to where water and fatare almost opposed-phase and in-phase, respectively.

Cortical bone may be segmented from the calculated relative differencebetween the magnitude information of echo one (MD and the reconstructedin-phase image by an empirically determined global threshold aftermasking out air areas, potentially by thresholding. Soft tissue andadipose tissue decomposition may be achieved by applying a three pointDixon signal modeling technique using the magnitude and the unwrappedphase information of all three echoes. This single acquisition mayprovide 5 or more sets of images:

1. images of bone

2. water-only images (i.e., fat-saturated images)

3. fat-only images (i.e., water-saturated images)

4. in-phase images

5. opposed-phase images

Embodiments of the invention may also generate a tissue mask of an MRimaging volume which represents relevant anatomical structures indifferent colors or grayscale values.

Embodiments of the invention may create a bulk density map of an MRimaging volume which can be used to create a does plan for treatment.

A ‘computer-readable storage medium’ as used herein encompasses anytangible storage medium which may store instructions which areexecutable by a processor of a computing device. The computer-readablestorage medium may be referred to as a computer-readable non-transitorystorage medium. The computer-readable storage medium may also bereferred to as a tangible computer-readable medium. In some embodiments,a computer-readable storage medium may also be able to store data whichis able to be accessed by the processor of the computing device.Examples of computer-readable storage media include, but are not limitedto: a floppy disk, a magnetic hard disk drive, a solid state hard disk,flash memory, a USB thumb drive, Random Access Memory (RAM), Read OnlyMemory (ROM), an optical disk, a magneto-optical disk, and the registerfile of the processor. Examples of optical disks include Compact Disks(CD) and Digital Versatile Disks (DVD), for example CD-ROM, CD-RW, CD-R,DVD-ROM, DVD-RW, or DVD-R disks. The term computer readable-storagemedium also refers to various types of recording media capable of beingaccessed by the computer device via a network or communication link. Forexample a data may be retrieved over a modem, over the internet, or overa local area network. References to a computer-readable storage mediumshould be interpreted as possibly being multiple computer-readablestorage mediums. Various executable components of a program or programsmay be stored in different locations. The computer-readable storagemedium may for instance be multiple computer-readable storage mediumwithin the same computer system. The computer-readable storage mediummay also be computer-readable storage medium distributed amongstmultiple computer systems or computing devices.

‘Computer memory’ or ‘memory’ is an example of a computer-readablestorage medium. Computer memory is any memory which is directlyaccessible to a processor. Examples of computer memory include, but arenot limited to: RAM memory, registers, and register files. References to‘computer memory’ or ‘memory’ should be interpreted as possibly beingmultiple memories. The memory may for instance be multiple memorieswithin the same computer system. The memory may also be multiplememories distributed amongst multiple computer systems or computingdevices.

‘Computer storage’ or ‘storage’ is an example of a computer-readablestorage medium. Computer storage is any non-volatile computer-readablestorage medium. Examples of computer storage include, but are notlimited to: a hard disk drive, a USB thumb drive, a floppy drive, asmart card, a DVD, a CD-ROM, and a solid state hard drive. In someembodiments computer storage may also be computer memory or vice versa.References to ‘computer storage’ or ‘storage’ should be interpreted aspossibly including multiple storage devices or components. For instance,the storage may include multiple storage devices within the samecomputer system or computing device. The storage may also includemultiple storages distributed amongst multiple computer systems orcomputing devices.

A ‘processor’ as used herein encompasses an electronic component whichis able to execute a program or machine executable instruction.References to the computing device comprising “a processor” should beinterpreted as possibly containing more than one processor or processingcore. The processor may for instance be a multi-core processor. Aprocessor may also refer to a collection of processors within a singlecomputer system or distributed amongst multiple computer systems. Theterm computing device should also be interpreted to possibly refer to acollection or network of computing devices each comprising a processoror processors. Many programs have their instructions performed bymultiple processors that may be within the same computing device orwhich may even be distributed across multiple computing devices.

A ‘user interface’ as used herein is an interface which allows a user oroperator to interact with a computer or computer system. A ‘userinterface’ may also be referred to as a ‘human interface device.’ A userinterface may provide information or data to the operator and/or receiveinformation or data from the operator. A user interface may enable inputfrom an operator to be received by the computer and may provide outputto the user from the computer. In other words, the user interface mayallow an operator to control or manipulate a computer and the interfacemay allow the computer indicate the effects of the operator's control ormanipulation. The display of data or information on a display or agraphical user interface is an example of providing information to anoperator. The receiving of data through a keyboard, mouse, trackball,touchpad, pointing stick, graphics tablet, joystick, gamepad, webcam,headset, gear sticks, steering wheel, pedals, wired glove, dance pad,remote control, and accelerometer are all examples of user interfacecomponents which enable the receiving of information or data from anoperator.

A ‘hardware interface’ as used herein encompasses an interface whichenables the processor of a computer system to interact with and/orcontrol an external computing device and/or apparatus. A hardwareinterface may allow a processor to send control signals or instructionsto an external computing device and/or apparatus. A hardware interfacemay also enable a processor to exchange data with an external computingdevice and/or apparatus. Examples of a hardware interface include, butare not limited to: a universal serial bus, IEEE 1394 port, parallelport, IEEE 1284 port, serial port, RS-232 port, IEEE-488 port, Bluetoothconnection, Wireless local area network connection, TCP/IP connection,Ethernet connection, control voltage interface, MIDI interface, analoginput interface, and digital input interface.

A ‘display’ or ‘display device’ as used herein encompasses an outputdevice or a user interface adapted for displaying images or data. Adisplay may output visual, audio, and or tactile data. Examples of adisplay include, but are not limited to: a computer monitor, atelevision screen, a touch screen, tactile electronic display, Braillescreen, Cathode ray tube (CRT), Storage tube, Bistable display,Electronic paper, Vector display, Flat panel display, Vacuum fluorescentdisplay (VF), Light-emitting diode (LED) displays, Electroluminescentdisplay (ELD), Plasma display panels (PDP), Liquid crystal display(LCD), Organic light-emitting diode displays (OLED), a projector, andHead-mounted display.

Radio-isotope imaging data is defined herein as two or three dimensionaldata that has been acquired using a medical imaging scanner that isconfigured to detect the radioactive decay of radioisotopes. Aradio-isotope imaging system is defined herein as an apparatus adaptedfor acquiring information about the physical structure of a patient andconstruct sets of two dimensional or three dimensional medical imagedata by detecting radiation emitted by radioactive markers or traceswithin the patient. Radio-isotope imaging data can be used to constructvisualizations which are useful for diagnosis by a physician. Thisvisualization can be performed using a computer.

Magnetic Resonance (MR) data is defined herein as being the recordedmeasurements of radio frequency signals emitted by atomic spins by theantenna of a Magnetic resonance apparatus during a magnetic resonanceimaging scan. A Magnetic Resonance Imaging (MRI) image is defined hereinas being the reconstructed two or three dimensional visualization ofanatomic data contained within the magnetic resonance imaging data. Thisvisualization can be performed using a computer.

In one aspect the invention provides an apparatus comprising: a magneticresonance imaging system which acquires magnetic resonance data from animaging volume; a processor for controlling the apparatus; and a memorycontaining machine executable instructions and a pulse sequence. Themagnetic resonance data is acquired using the pulse sequence includesgradient echo data. Execution of the machine executable instructionscauses the processor to: acquire the magnetic resonance data using themagnetic resonance imaging system and the pulse sequence; and segmentthe magnetic resonance data into a plurality of segments, including afat segment, a water segment, a cortical bone segment, and an airsegment; and create a bulk density map of the imaging volume from thesegments.

The processor may be replaced by a controller or a control system.

A pulse sequence as used herein can encompass a set of instructions oroperations performed as a function of time which together may be used tocontrol or to generate commands for controlling the magnetic resonanceimaging system to acquire the magnetic resonance data. The pulsesequence can be in a machine executable form or it can be in a graphicalform which is adapted for manipulation or change by a human operator ona graphical user interface. If in graphical form the pulse sequence maybe converted into a machine executable form by a suitable program orprogram module.

In some embodiments, the magnetic resonance data acquired using thepulse sequence may include free induction decay data and gradient echodata. Free induction decay data as used herein encompasses a measurementof the free induction decay curve measured during the acquisition of themagnetic resonance data. The free induction decay data may for instancebe free induction decay which decays in a characteristic time constantT2 or T2*. An echo signal is a signal which is generated from a freeinduction decay using a bipolar switched magnetic gradient. There is anecho which is produced when the magnetic field gradient is reversed.Gradient echo data as used herein encompasses the measurement recordingof such an echo signal. Gradient echo data as used herein encompassesthe recording of one or more echo signals.

Execution of the machine executable instructions can cause the processorto acquire the magnetic resonance data using the magnetic resonanceimaging system in accordance with the pulse sequence. This is to saythat the pulse sequence commands or control sequences can be used tocontrol the magnetic resonance imaging system to acquire the magneticresonance data.

A fat segment, which also may be referred to as a water-saturatedsegment, can indicate the concentration or location of fat or adiposetissue within the imaging volume.

Likewise, a water segment, which also may be referred to as afat-saturated segment, can show the concentration or location of waterprotons, with the fat protons removed, within the imaging volume.

A cortical bone segment can encompass magnetic resonance data whichcontains free induction decay data which is descriptive of thelocation(s) of cortical bone within the imaging volume.

Similarly, an air segment can encompass magnetic resonance data which isdescriptive of the location(s) of air within the imaging volume.

In some embodiments, an ultra-short echo time image can be used fordifferentiating between bone and air.

In some embodiments, execution of the instructions can further cause theprocessor to create the bulk density map from the segments by:determining for each of a plurality of voxels of the imaging volume,which element among fat, water, cortical bone and air segment isprimarily represented in the voxel; and assigning a corresponding bulkdensity value to each voxel, where the assigned bulk density valuedepends on which element among fat, water, cortical bone and air isprimarily represented in the voxel.

In some embodiments, execution of the instructions can further cause theprocessor to create the bulk density map from the segments by: assigningcorresponding bulk density values to fat, water, cortical bone and air;determining, for each of a plurality of voxels of the imaging volume, aplurality of fractions which pertain to the voxel, including a fatfraction, a water fraction, a cortical bone fraction, and an airfraction; and for each of the plurality of voxels, weighting each of theplurality of fractions by the corresponding bulk density value.

In some embodiments, execution of the instructions can further cause theprocessor to generate one or more digitally reconstructed radiographs(DRRs) from the magnetic resonance data.

In some versions of these embodiments, execution of the instructions canfurther cause the processor to transfer the one or more DRRs to aradiation treatment planning system.

In some embodiments, execution of the instructions can further cause theprocessor to generate an artificial computed tomography image based onfractions of fat, water, air, and cortical bone in each voxel of theimaging volume.

In some embodiments, execution of the instructions can further cause theprocessor to reconstruct an in-phase image, a fat-saturated image, awater-saturated image, and an ultra-short echo time image, and toproduce the cortical bone segment by subtracting the in-phase image fromthe ultra-short echo time image.

In some embodiments, execution of the instructions can further cause theprocessor to reconstruct an opposed phase image from the magneticresonance data. An opposed phase image as used herein encompasses animage with a signal from two distinct components such as fat and watersignals are 180 degrees out of phase which causes the destructiveinterference of the nuclear magnetic resonance signal within aparticular voxel. This embodiment may be beneficial when performingradiation therapy planning on particular types of tissue. For instanceit may be beneficial in identifying lesions in the liver or the adrenalglands. It may also be beneficial for identifying the variouspathological regions in the brain. The opposed phase image may forinstance be displayed on the graphical user interface during theradiation therapy planning or it may for instance be used as an inputfor the radiation therapy planning program module.

In some embodiments, execution of the instructions can further cause theprocessor to reconstruct one or more echo images. An echo image is animage reconstructed from the recorded magnetic resonance data of agradient echo. Echo images are images each reconstructed from themagnetic resonance data of multiple gradient echoes. The in-phase image,the fat-saturated image, the water-saturated image, and the ultra-shortecho time image are constructed from the magnetic resonance data using aDixon signal model. For instance the Dixon signal model may be atwo-point Dixon signal model, a three-point Dixon signal model, or afour-point Dixon signal model. This embodiment may be advantageousbecause this provides for an effective and accurate means ofconstructing these images. The three-point Dixon signal model may beused in some embodiments to reconstruct the opposed phase image from themagnetic resonance data at the same time that the other images are alsoreconstructed

An in-phase image as used herein can encompass an image reconstructedfrom magnetic resonance data that comprises the T1 and regular protonweighted image.

An ultra-short echo time image as used herein can encompass an imagereconstructed from a free induction decay data where the free inductiondecay occurred on an extremely short timescale. The free induction decaymay have a time constant on the order of several hundreds ofmicroseconds. The ultra-short echo time enables the imaging of tissuewith extremely small free induction decay values such as tendons orbone.

In some embodiments, execution of the instructions can further cause theprocessor to reconstruct an in-phase image, a fat-saturated image, awater-saturated image, and an ultra-short echo time image from themagnetic resonance data, and to produce the cortical bone segment byautomatically thresholding a noise level in the in-phase image andsubsequently removing background noise.

In some versions of these embodiments, execution of the instructions canfurther cause the processor to produce the cortical bone segment byregistering the in-phase image with a bone probability atlas.

In some embodiments, execution of the instructions can further cause theprocessor to transfer the bulk density map to a radiation treatmentplanning system.

In some embodiments, execution of the instructions can further cause theprocessor to display a fat segment, a water segment, a cortical bonesegment and an air segment of magnetic imaging data from an imagingvolume on a graphical user interface.

In some embodiments, execution of the instructions can further cause theprocessor to receive radiation therapy planning data from a graphicaluser interface. In some embodiments the electron bulk density map and/orone or more DRRs can be used along with input from the graphical userinterface to calculate the radiation therapy planning data. Thisembodiment may be particularly beneficial because the data necessary foran operator or a physician to plan a radiation session or therapy isdisplayed on the graphical user interface. The user or operator maystudy the images and then use a mouse or other human input device tomanipulate shapes and controls on the graphical user interface. Theuser's entry may then be translated into the radiation therapy planningdata. This embodiment may be particularly beneficial because the datanecessary for performing the radiation therapy may have been presentedand acquired in a single magnetic resonance acquisition. This may resultin an increase in the speed in which radiation therapy planning can beperformed.

In another embodiment execution of the instructions can further causethe processor to generate radiation therapy planning data using theelectron bulk density mask and/or one or more DRRs, and a treatment planusing a radiation therapy planning program module. A treatment plan asused herein encompasses a data file descriptive of a plan for performinga radiation therapy. For instance the treatment plan may containanatomical data descriptive of the patient or subject in conjunctionwith regions of the subject to be treated. The radiation therapyplanning program module may contain executable code which is able tointerpret the treatment plan and register it to at least one of theelectron bulk density mask and/or one or more DRRs. This embodiment mayhave the advantage that the medical apparatus is able to acquire themagnetic resonance data and then proceed with planning and executing aradiation therapy on the patient or subject

In some embodiments the apparatus can further include a radiationtherapy system. Execution of the instructions can further cause theprocessor to generate radiation therapy control commands using theradiation therapy planning data. Execution of the instructions canfurther cause the processor to treat the subject with the radiationtherapy system by executing the radiation therapy control commands. Theradiation therapy control commands as used herein encompass machineexecutable commands which control a radiation therapy system.

In some embodiments the radiation therapy system can be a linearaccelerator.

In some embodiments the radiation therapy system can be a gamma knife.

In some embodiments the radiation therapy system can be a chargedparticle therapy system. A charged particle therapy system as usedherein is a system which is adapted for shooting charged particles suchas charged nuclei or molecules at a target region of the subject. Forexample carbon nuclei or protons may be directed at a target zone of thesubject.

In some embodiments the radiation therapy system can be a proton therapysystem. A proton therapy system as used herein is a therapy system whichis adapted for shooting proton such as hydrogen nuclei at a target zoneof the subject.

In some embodiments the radiation therapy system can be an x-ray therapysystem. An x-ray therapy system as used herein encompasses a system fordirecting x-rays in a target zone of a subject for performing radiationtherapy.

In some embodiments the radiation therapy system can be an external beamradiation system. An external beam radiation system as used hereinencompasses a radiation therapy system for directing an externalradiation beam at a target zone of a subject.

In some embodiments the radiation therapy system can be a brachytherapysystem.

Another aspect the invention provides a method of operating anapparatus, such as a medical apparatus. The method includes: acquiringmagnetic resonance data from an imaging volume via a magnetic resonanceimaging system and a pulse sequence, wherein the magnetic resonance dataincludes gradient echo data; segmenting the magnetic resonance data intoa plurality of segments, the segments including a fat segment, a watersegment, a cortical bone segment, and an air segment; and creating abulk density map of the imaging volume from the segments.

In some embodiments, creating the bulk density map from the segments cancomprise: determining, for each of a plurality of voxels of the imagingvolume, which element among fat, water, air and cortical bone isprimarily represented in the voxel; and assigning a corresponding bulkdensity value to each voxel, where the assigned bulk density valuedepends on which element among fat, water, cortical bone, and air isprimarily represented in the voxel.

In some embodiments, creating the bulk density map from the segments cancomprise: assigning corresponding bulk density values to fat, water,cortical bone and air; determining, for each of a plurality of voxels ofthe imaging volume, a plurality of fractions which pertain to the voxel,including an a fat fraction, a water fraction, a cortical bone fractionand an air fraction; and for each of the plurality of voxels, weightingeach of the plurality of fractions by the corresponding bulk densityvalue.

In some embodiments, the method can further comprise generating one ormore digitally reconstructed radiographs (DRRs) from the magneticresonance data.

In some versions of these embodiments, the method can further comprisetransferring the one or more DRRs to a radiation treatment planningsystem.

In some embodiments, the method can further comprise generating anartificial computed tomography image based on fractions of fat, water,cortical bone, and air in each voxel of the imaging volume.

In some embodiments, the method can further comprise: reconstructing anin-phase image, a fat-saturated image, a water-saturated image, and anultra-short echo time image from the magnetic resonance data; andproducing the cortical bone segment by subtracting the in-phase imagefrom the ultra-short echo time image.

In some embodiments, the method can further comprise: reconstructing anin-phase image, a fat-saturated image, a water-saturated image, and anultra-short echo time image from the magnetic resonance data; andproducing the cortical bone segment by automatically thresholding anoise level in the in-phase image and subsequently removing backgroundnoise.

In some embodiments, producing the cortical bone segment can furthercomprise registering the in-phase image with a bone probability atlas.

Yet another aspect of the invention provides a non-transitorycomputer-readable storage medium. The non-transitory computer-readablestorage medium has stored therein a pulse sequence and machine readableinstructions configured to be executed by a processor to control anapparatus including a magnetic resonance imaging system. The machinereadable instructions are configured in conjunction with the pulsesequence to cause the apparatus to execute a process. The processcomprises: acquiring magnetic resonance data from an imaging volumeusing the magnetic resonance imaging system and the pulse sequence,wherein the magnetic resonance data includes gradient echo data;segmenting the magnetic resonance data into a plurality of segments byexecuting a set of instructions, the segments including a fat segment, awater segment, a cortical bone segment, and an air segment; and creatinga bulk density map of the imaging volume from the segments.

BRIEF DESCRIPTION OF THE DRAWINGS

The present invention will be more readily understood from the detaileddescription of exemplary embodiments presented below considered inconjunction with the accompanying drawings, as follows.

FIG. 1 shows a flow chart which illustrates an embodiment of a method ofacquiring and processing magnetic resonance data.

FIG. 2 shows a flow chart which illustrates a further embodiment of amethod of acquiring and processing magnetic resonance data.

FIG. 3 illustrates a pulse sequence in the form of a timing diagram.

FIG. 4 shows a cortical bone image.

FIG. 5 shows a medullary bone image.

FIG. 6 shows a complete bone image.

FIG. 7 shows a fat-saturated image.

FIG. 8 shows an in-phase image.

FIG. 9 shows the ultra-short echo time phase image.

FIG. 10 shows a block diagram which illustrates one embodiment of amedical apparatus.

FIG. 11 shows a block diagram which illustrates another embodiment of amedical apparatus.

FIG. 12 shows a block diagram which illustrates a further embodiment ofa medical apparatus.

FIG. 13 shows images for four subjects which include DigitalReconstructed Radiographs (DRRs).

FIG. 14 shows a flow chart which illustrates an embodiment of a methodof acquiring magnetic resonance data and processing the magneticresonance data for treatment planning.

FIG. 15 shows a flow chart which illustrates another embodiment of amethod of acquiring magnetic resonance data and processing the magneticresonance data for treatment planning.

FIG. 16 shows a flow chart which illustrates yet another embodiment of amethod of acquiring magnetic resonance data and processing the magneticresonance data for treatment planning.

FIG. 17 shows some example images which may be generated from magneticimage data for treatment planning.

FIG. 18 shows yet another embodiment of a medical apparatus.

FIG. 19 illustrates an example embodiment of operations which may beperformed by a system and method which acquire magnetic resonance dataand process the magnetic resonance data for treatment planning.

FIG. 20 shows an example embodiment of modules and a corresponding workflow for a system and method which acquire magnetic resonance data andprocess the magnetic resonance data for treatment planning.

DETAILED DESCRIPTION

The present invention will now be described more fully hereinafter withreference to the accompanying drawings, in which embodiments of thepresent invention are shown. The present invention may, however, beembodied in different forms and should not be construed as limited tothe embodiments set forth herein. Rather, these embodiments are providedas teaching examples of the invention. Within the present disclosure andclaims, when something is said to have approximately a certain value,then it means that it is within 10% of that value, and when something issaid to have about a certain value, then it means that it is within 25%of that value.

Like numbered elements in these figures are either equivalent elementsor perform the same function. Elements which have been discussedpreviously will not necessarily be discussed in later figures if thefunction is equivalent.

FIG. 1 shows a flow diagram which illustrates a method of acquiring andprocessing magnetic resonance data. In step 100 magnetic resonance datais acquired using an MRI system and a pulse sequence. The pulse sequencemay for instance be a pulse sequence as is demonstrated in FIG. 3. Nextin step 102 an in-phase image, a fat-saturated image, a water-saturatedimage, and an ultra-short echo time image may be reconstructed from themagnetic resonance data. The ultra-short echo time image comprises boneimage data.

FIG. 2 shows a block diagram which illustrates a further embodiment of amethod of acquiring and processing magnetic resonance data. In step 200magnetic resonance data is acquired using the MRI system and a pulsesequence. In step 202 an in-phase image, a fat-saturated image, awater-saturated image, and an ultra-short echo time image arereconstructed from the magnetic resonance imaging data. The ultra-shortecho time image comprises bone image data. A bone image data is imagedata which is descriptive of the anatomy of bone tissue within a patientor a subject. In step 204 a medullary bone image is constructed from thewater-saturated image. In some embodiments this step may includeremoving information from the image using a model, for instance removingadipose tissue from the image. Next in step 206 a cortical bone image isconstructed by subtracting the in-phase image from the ultra-short echotime image. Next in step 208 a complete bone image is constructed byadding the medullary bone image to the cortical bone image. Finally instep 210 a spatially dependent radiation attenuation coefficient iscalculated. In step 210 this may include using the complete bone image,the fat-saturated image, the in-phase image, and/or the ultra-short echotime image.

FIG. 3 illustrates a pulse sequence 300 in the form of a timing diagram.In this pulse sequence 300 there are four timelines, there is timeline302 which illustrates when radio frequency energy is applied. Timeline304 illustrates the readout gradient. Timeline 306 illustrates a gatefor data acquisition. Timeline 308 illustrates the nuclear magneticresonance signal. On timeline 302 a radio frequency pulse 310 is appliedduring time Trf. On timeline 308 a free induction decay 314, a firstgradient echo 316 and a second gradient echo 318 are shown. On timeline308 there are three gradient pulses. Timeline 304 shows when a firstgradient pulse 320, a second gradient pulse 322, and a third gradientpulse 324 are applied. The first gradient pulse 320 is applied duringthe free induction decay 314. The second gradient pulse 322 causes thefirst gradient echo 316. The third gradient pulse 324 causes the secondgradient echo 318. The characteristic time rate at which the freeinduction decay 314 decays such as the T1, the T2, or T2* time constantis indicated as TE1 326. The first gradient echo 316 has a maximum atTE2 328. The second gradient echo 318 has a maximum at TE3 330.

Timeline 306 shows when magnetic resonance data is acquired. The freeinduction decay data is acquired during time interval Taq1 332. Thefirst gradient echo data is acquired during time interval 334. Thesecond gradient echo data is acquired during time interval 336. Thepulse sequence illustrated in FIG. 3 is representative. Changes in thepulse sequence may be made. For instance the time when the freeinduction decay data is acquired may be delayed until the time marked338.

In the example shown in FIG. 3, the echo times are chosen such that theecho times are acquired at in-phase and opposed-phase times. However,they do not need to be in-phase of opposed-phase echo times. Anappropriate Dixon model may be used such that the gradient echoes may beacquired at non-specific echo time. For instance, various Dixon modelswill work for 2, 3, or 4 non-specific echo times.

FIG. 4 shows an example of a cortical bone image 400. In this image 400cortical bone 402 is shown. The cortical bone image 400 was constructedby subtracting a scaled multiple (k) of the in-phase image (IP) from theultra-short echo time image (UTE) (i.e., UTE−k*IP, where k could be 1 oranother appropriate scale factor).

FIG. 5 shows a fat-only (water-saturated) image 500. Medullary bone 502is clearly shown in the fat-only image 500. Image 500 includes medullarybone and subcutaneous fat.

FIG. 6 shows a bone image 600 that was constructed by adding images 400and 500. Image 600 includes cortical bone, medullary bone, andsubcutaneous fat. In region 602 cortical plus medullary bone is shown.

FIG. 7 shows a fat-saturated image 700.

FIG. 8 shows an in-phase image 800.

FIG. 9 shows the ultra-short echo time image 900 for phase. An aircavity 902 is visible in this image.

FIG. 10 shows a block diagram which illustrates a medical apparatus1000. The medical apparatus 1000 comprises a magnetic resonance imagingsystem 1002. The magnetic resonance imaging system 1002 is shown ascomprising a magnet 1004. The magnet 1004 shown in FIG. 10 is acylindrical type superconducting magnet. The magnet 1004 has a liquidhelium cooled cryostat with superconducting coils. It is also possibleto use permanent or resistive magnets. The use of different types ofmagnets is also possible for instance it is also possible to use both asplit cylindrical magnet and a so called open magnet. A splitcylindrical magnet is similar to a standard cylindrical magnet, exceptthat the cryostat has been split into two sections to allow access tothe iso-plane of the magnet, such magnets may for instance be used inconjunction with charged particle beam therapy. An open magnet has twomagnet sections, one above the other with a space in-between that islarge enough to receive a subject: the arrangement of the two sectionsarea similar to that of a Helmholtz coil. Open magnets are popular,because the subject is less confined. Inside the cryostat of thecylindrical magnet there is a collection of superconducting coils.Within the bore 1006 of the cylindrical magnet 1004 there is an imagingzone 1008 where the magnetic field is strong and uniform enough toperform magnetic resonance imaging.

Within the bore 1006 of the magnet 1004 there is also a magnetic fieldgradient coil 1010 which is used for acquisition of magnetic resonancedata to spatially encode magnetic spins within the imaging zone 1008 ofthe magnet 1004. The magnetic field gradient coil 1010 is connected to amagnetic field gradient coil power supply 1012. The magnetic fieldgradient coil 1010 is intended to be representative. Typically magneticfield gradient coils 1010 contain three separate sets of coils forspatially encoding in three orthogonal spatial directions. A magneticfield gradient power supply supplies current to the magnetic fieldgradient coils. The current supplied to the magnetic field coils iscontrolled as a function of time and may be ramped or pulsed.

Adjacent to the imaging zone 1008 is a radio frequency coil 1014 formanipulating the orientations of magnetic spins within the imaging zone1008 and for receiving radio transmissions from spins also within theimaging zone 1008. The radio frequency coil may contain multiple coilelements. The radio frequency coil or each of any multiple coil elementsmay also be referred to as a channel. The radio frequency coil may alsobe referred to as an antenna. The radio frequency coil 1014 is connectedto a radio frequency transceiver 1016. The radio frequency coil 1014 andradio frequency transceiver 1016 may be replaced by separate transmitand receive coils and a separate transmitter and receiver. It isunderstood that the radio frequency coil 1014 and the radio frequencytransceiver 1016 are representative. The radio frequency coil 1014 isintended to also represent a dedicated transmit antenna and a dedicatedreceive antenna. Likewise the transceiver 1016 may also represent aseparate transmitter and receivers.

The transceiver 1016 and the magnetic field gradient coil power supply1012 are connected to a hardware interface 1024 of a computer system1022. The computer system 1022 further comprises a processor 1026. Theprocessor is connected to the hardware interface 1024 which enables theprocessor 1026 to control the operation and function of the medicalapparatus 1000. The processor 1026 is further connected to userinterface 1028. The processor 1026 is also connected to computer storage1030 and computer memory 1032.

The computer storage 1030 is shown as containing a pulse sequence 1034.The pulse sequence 1034 may be used for controlling the magneticresonance imaging system 1002. The computer storage 1030 is shown asfurther containing magnetic resonance data 1036 that was acquired fromthe magnetic resonance imaging system 1002 using the pulse sequence1034. The computer storage 1030 is further shown as containing anin-phase image 1038, a fat-saturated image 1040, a water-saturated image1042 and an ultra-short echo time image 1044 that was reconstructed fromthe magnetic resonance data 1036. The computer storage 1030 is alsoshown as containing an opposed phase image 1046 that was reconstructedfrom the magnetic resonance data 1036. The opposed phase image 1046 isnot calculated or reconstructed in all embodiments.

The computer storage 1030 is further shown as containing a medullarybone image 1048 reconstructed from the water-saturated image 1042. Thecomputer storage 1030 is further shown as containing a cortical boneimage 1050 reconstructed by subtracting the in-phase image 1038 from theultra-short echo time image 1044. The computer storage 1030 is shown asfurther containing a complete bone image 1052 which is constructed byadding the medullary bone image 1048 to the cortical bone image 1050.The computer storage 1030 is shown as containing a spatially dependentradiation attenuation coefficient 1054 which is not present in allembodiments. The computer storage 1030 is further shown as containing aradiation therapy planning data 1056. The radiation therapy planningdata 1056 is optional and is not present in all embodiments. Thecomputer storage 1030 is further shown as containing a treatment plan1058 which is optional also.

The computer memory 1032 contains computer executable instructions forcontrolling the operation and functioning of the medical apparatus 1000.The computer memory 1032 is shown as containing a control module 1060.The control module 1060 contains computer executable code which allowsthe processor 1026 to control the operation and function of the medicalapparatus 1000. The computer storage 1032 is further shown as containingan image reconstruction module 1062. The image reconstruction module1062 contains computer executable code for reconstructing the images1038, 1040, 1042, 1044, 1046 contained within the computer storage 1030.The computer memory 1032 further contains an image manipulation module1064 which allows the processor 1026 to manipulate such as adding andsubtracting images.

The computer memory 1032 is shown as optionally containing a three-pointDixon signal model 1066 which may be used by the image reconstructionmodule 1062. The computer memory 1032 is further shown as containing animage segmentation module 1068. In some embodiments the imagesegmentation module may be used to segment any of the images containedwithin the computer storage 1030. The computer memory 1032 is furthershown as containing the radiation attenuation coefficient calculationmodule 1070. The radiation attenuation coefficient calculation module1070 may in some embodiments be used to calculate the spatiallydependent radiation attenuation coefficient 1054 from the complete boneimage 1052, the fat-saturated image 1040, the in-phase image 1038, andthe ultra-short echo time image 1044.

In some embodiments there may be a radiation therapy planning datageneration module 1072 present in the computer memory 1032. Theradiation therapy planning generation module 1072 is adapted forautomatically generating the radiation therapy planning data 1056 usingthe treatment plan 1058 and the spatially dependent radiationattenuation coefficient 1054. Some embodiments may also have a graphicaluser interface control module 1074 present in the computer memory 1032for controlling the operation and function of a graphical user interface1076. The optional graphical user interface 1076 is shown as displayinga complete bone image 600, a fat-saturated image 700, an in-phase image800, and an ultra-short echo time image 900. The graphical userinterface 1076 further contains a radiation therapy planning interface1078 where an operator or physician may enter radiation therapy planningdata 1056.

FIG. 11 shows an embodiment of a medical apparatus 1100 similar to thatshown in FIG. 10. The medical apparatus shown in FIG. 11 includes aradiation therapy system 1122. The magnet 1004 is a superconductingmagnet and includes a cryostat 1124 with several superconducting coils1126. There is also a compensation coil 1128 which creates an area ofreduced magnetic field 1130 which surrounds the magnet 1004. Theradiation therapy system 1122 in this embodiment is intended to berepresentative of radiation therapy systems in general. The componentsshown here are typical for LINAC and x-ray therapy systems. However withminor modifications such as using a split magnet charged particles orbeta particle radiation therapy systems can also be illustrated usingthis diagram. There is a gantry 1132 which is used to rotate aradiotherapy source 1134 about the magnet 1004. The gantry 1132 isrotated about the axis of rotation 1133 by a rotation actuator 1135.There is a radiation therapy source 1134 which is rotated by the gantry1132. The radiotherapy source 1134 generates a radiation beam 1138 whichpasses through collimator 1136. In FIG. 11, a target zone labeled 1142which is irradiated by the radiation beam 1138 is shown. As theradiation source 1134 rotates about the axis of rotation 1133 the targetzone 1142 is irradiated. There is also a support positioning system 1140for positioning the support 1020 to optimize the location of the targetzone 1142 relative to the radiation therapy system 1122.

The hardware interface 1024 is shown as being connected to thetransceiver 1016, the power supply 1012, the rotation actuator 1135, andthe support positioning system 1140. The hardware interface 1024 allowsthe processor 1026 to send and receive control signals to all of thesecomponents 1012, 1016, 1135, 1140.

The computer storage 1030 is shown as containing radiation therapycontrol commands 1150. The radiation therapy control commands 1150comprise instructions that when executed by the radiation therapy system1122 cause the radiation therapy system 1122 to treat the target zone1142. The computer memory 1032 is shown as containing a radiationtherapy control command generation module 1152. The radiation therapycontrol command generation module 1152 contains instructions which allowthe processor 1026 to generate the radiation therapy control commands1150 from the radiation therapy planning data 1056.

FIG. 12 illustrates a medical apparatus 1200 similar to that shown inFIG. 10. In this embodiment a radio isotope imaging system 1202 has beenintegrated into the medical apparatus 1200. The radio-isotope imagingsystem 1202 comprises a scintillator ring 1204 adapted for detectingionizing radiation. The individual scintillators which make up thescintillator ring may be connected to a set of light pipes 1206 or fiberoptics which are led out of the magnet 1004 to a series of lightdetectors 1208. Within the subject 1018 is shown a concentration ofradio-isotope 1210. Ionizing radiation is emitted 1212 and is absorbedin the scintillator ring 1204. Within the computer storage 1030 is shownthe radio-isotope imaging data 1220. The radio-isotope imaging data 1220is the recorded data acquired by the light detectors 1208. The computerstorage 1030 is further shown as containing a medical image 1222. Themedical image is an image, reconstruction, or rendering of theradio-isotope imaging data which is descriptive of the location ofradio-isotope 1210 within the subject.

The medical image 1222 was reconstructed from the radio-isotope imagingdata 1220. The radio-isotope imaging system 1202 may for instance be apositron emission tomography system or a single photon emission computertomography system. The computer memory 1032 is shown as containing amedical image reconstruction module 1230. The medical imagereconstruction module 1230 contains computer executable code which theprocessor 1026 may use to reconstruct the medical image 1222 from theradio-isotope imaging data 1220. The computers 1022 shown in theembodiments of FIGS. 10, 11, and 12 are equivalent as is the softwareand data stored within the computer memory 1032 and computer storage1030 respectively.

FIG. 13 shows images for four subjects. Each row includes images for onesubject generated by the single imaging sequence. The columns of imagesfrom left to right include bone-enhanced images 400, water-only images700, in-phase images 800, opposed-phase images 1046, fat-only images500, and digital reconstructed radiographs (DRRs) 1240. The boneenhanced images 400 contrast cortical bone corresponding to FIG. 4 andare constructed by subtracting the in-phase image 800 from theultra-short echo time image corresponding to FIG. 9. The differencebetween the images of FIG. 4 and the column of bone enhanced imagesincludes a weighting of the in-phase image which reduces the presence ofthe brain. The water-only images 700 are T1w images with fat-saturationcorresponding to FIG. 7. The in-phase images 800 correspond to FIG. 8.The fat-only images 500 correspond to FIG. 5 and include medullary bone.The last column includes the DRRs 1240. The DRR is constructed as a2-dimensional projection of the 3-dimensional volume of the bone-enhanceimage 400. Alternatively, the DRR is constructed as a 2-dimensionalprojection of the weighted in-phase image subtracted from theultra-short echo time image. The projections are shown as sagittalperspectives. The DRRs are of sufficient quality to be used in2-dimensional patient matching. Patient matching is used to position thesubject 1018 in radiation therapy. Adjustments to the subject 1018position are done by the support positioning system 1140. The DRR imagescan replace conventional CT images.

In another embodiment, the bone enhanced image or cortical bone imageare used to register the images with other images including otherimaging modalities such as PET, SPECT, CT, etc. The images generatedfrom the pulse sequence 300 are inherently registered. The bone-enhancedimages provide both registration and density information forattenuation. Furthermore, the generated MR images from the pulsesequence include soft-tissue images which further enhance attenuation.

FIG. 14 shows a flow chart which illustrates an embodiment of a method1400 of acquiring magnetic resonance data and processing the magneticresonance data for treatment planning.

In an operation 1405, magnetic resonance data is acquired using an MRIsystem and a pulse sequence. In some embodiments, the pulse sequence mayfor instance be a pulse sequence as is illustrated in FIG. 3. In someembodiments, the free induction decay data for the ultra-short echo timeimage may be omitted, for example when the imaging volume is a pelvicarea or other area where no cortical bone/air adjacencies are expectedto exist such that bone and air segments may be separated, for example,by reference to a priori knowledge of human anatomy (e.g., by use of abone probability atlas).

In an operation 1410 the magnetic resonance data is segmented into a fatsegment, a water segment, a cortical bone segment, and an air segment.In some embodiments, the fat segment and the water segment may beobtained via a Dixon acquisition. In some embodiments, the cortical bonesegment may be obtained as explained above by subtracting an in-phaseimage from an ultra-short echo time image. In other embodiments, thecortical bone segment may be obtained by inverting the in-phase imageand registration with a bone probability atlas. In some embodiments, theair segment may be obtained by adding the in-phase image to a corticalbone image generated according to embodiments set forth above.

In an operation 1415, a bulk density map (i.e., an electron bulk densitymap) is created using the fat, water, cortical bone, and air segments.

In some embodiments, a predetermined bulk density value for fat isassigned to the fat segment, a predetermined bulk density value forwater is assigned to the water segment, a predetermined bulk densityvalue for cortical bone is assigned to the cortical bone segment, and apredetermined bulk density value for air is assigned to the air segment.Then, the various segments with the corresponding assigned bulk densityvalues may be combined to produce a bulk density map for the imagingvolume. In some embodiments, the predetermined bulk density values maybe determined based on empirical data for a plurality of individuals. Insome embodiments, the predetermined bulk density values may bedetermined at least in part based on characteristics of an individualpatient, which may include the patient's age, sex, etc.

In some embodiments, the bulk density map is created from the segmentsby: determining, for each of a plurality of voxels of the imagingvolume, which element among fat, water, cortical bone and air segment isprimarily represented in the voxel; and assigning a corresponding bulkdensity value to each voxel, where the assigned bulk density valuedepends on which element among fat, water, cortical bone and air isprimarily represented in the voxel.

In some embodiments, the bulk density map is created from the segmentsby: determining, for each of a plurality of voxels of the imagingvolume, a plurality of fractions which pertain to that voxel, includinga fat fraction, a water fraction, a cortical bone fraction, and an airfraction; and for each of the plurality of voxels, weighting each of theplurality of fractions by the corresponding bulk density value.

FIG. 15 shows a flow chart which illustrates another embodiment of amethod 1500 acquiring magnetic resonance data and processing themagnetic resonance data for treatment planning.

In an operation 1505, magnetic resonance data is acquired using an MRIsystem and a pulse sequence. In some embodiments, the pulse sequence mayfor instance be a pulse sequence as is illustrated in FIG. 3. In someembodiments, the free induction decay data for the ultra-short echo timeimage may be omitted, for example when the imaging volume is a pelvicarea or other area where no cortical bone/air adjacencies are expectedto exist such that bone and air segments may be separated, for example,by reference to a priori knowledge of human anatomy (e.g., by use of abone probability atlas).

In an operation 1510 the magnetic resonance data is segmented into a fatsegment, a water segment, a cortical bone segment, and an air segment.In some embodiments, the fat segment and the water segment may beobtained via a Dixon acquisition. In some embodiments, the cortical bonesegment may be obtained as explained above by subtracting an in-phaseimage from an ultra-short echo time image. In other embodiments when theimaging volume is a pelvic area or other area where no cortical bone/airadjacencies are expected to exist, the cortical bone segment may beobtained by inverting the in-phase image and registration with a boneprobability atlas. In some embodiments, the air segment may be obtainedby adding the in-phase image to a cortical bone image generatedaccording to embodiments set forth above.

In an operation 1515, a predetermined bulk density value for fat isassigned to the fat segment, a predetermined bulk density value forwater is assigned to the water segment, a predetermined bulk densityvalue for cortical bone is assigned to the cortical bone segment, and apredetermined bulk density value for air is assigned to the air segment.Then, the various segments with the corresponding assigned bulk densityvalues may be combined to produce a bulk density map for the imagingvolume. In some embodiments, the predetermined bulk density values maybe determined based on empirical data for a plurality of individuals. Insome embodiments, the predetermined bulk density values may bedetermined at least in part based on characteristics of an individualpatient, which may include the patient's age, sex, etc.

In an operation 1520, a bulk density map (i.e., an electron bulk densitymap) is created using the fat, water, cortical bone, and air segments.

In some embodiments, the bulk density map is created from the segmentsby: determining, for each of a plurality of voxels of the imagingvolume, which element among fat, water, cortical bone and air segment isprimarily represented in the voxel; and assigning a corresponding bulkdensity value to each voxel, where the assigned bulk density valuedepends on which element among fat, water, cortical bone and air isprimarily represented in the voxel.

In some embodiments, the bulk density map is created from the segmentsby: determining, for each of a plurality of voxels of the imagingvolume, a plurality of fractions which pertain to that voxel, includinga fat fraction, a water fraction, a cortical bone fraction, and an airfraction; and for each of the plurality of voxels, weighting each of theplurality of fractions by the corresponding bulk density value.

In an operation 1525, one or more digitally reconstructed radiographs(DRRs) are created using the electron bulk density map created inoperation 1520. In some embodiments, operation 1525 may be omitted.

In an operation 1530, one or more artificial computed tomography imagesare generated based on the fat, water, cortical bone, and air fractionsin each voxel. In some embodiments, operation 1530 may be omitted.

In an operation 1535, a bulk density map, one or more DRRS, and/or oneor more artificial computed tomography images are transferred to aradiation treatment planning system. In some embodiments, images may betransferred in accordance with the Digital Imaging and Communications inMedicine (DICOM) standard. In some embodiments, the DRRs may begenerated by a magnetic resonance imaging system or apparatus inoperation 1525, and transferred to a treatment planning system inoperation 1535. In other embodiments, DRRs may be generated by thetreatment planning system, for example using the electron bulk densitymap.

FIG. 16 shows a flow chart which illustrates yet another embodiment of amethod 1600 of acquiring magnetic resonance data and processing themagnetic resonance data for treatment planning.

In an operation 1605, magnetic resonance data is acquired using an MRIsystem and a pulse sequence. In some embodiments, the pulse sequence mayfor instance be a pulse sequence as is illustrated in FIG. 3. In someembodiments, the free induction decay data for the ultra-short echo timeimage may be omitted, for example when the imaging volume is a pelvicarea or other area where no cortical bone/air adjacencies are expectedto exist such that bone and air segments may be separated, for example,by reference to a priori knowledge of human anatomy (e.g., by use of abone probability atlas).

In an operation 1610, an in-phase image, a fat-saturated image, awater-saturated image, and an ultra-short echo time image arereconstructed from the magnetic resonance imaging data.

In an operation 1615, background noise is filtered or removed from thein-phase image. In some embodiments, background noise may be removed byautomatic intensity thresholding. In some embodiments, this may yieldbone-enhanced images. In some embodiments, operation 1615 may beomitted.

In an operation 1620, the in-phase image (or the noise-filtered in-phaseimage) is registered with a bone probability atlas. The bone probabilityatlas may have been generated based on magnetic resonance data generatedfor a plurality of sample patients or subjects. In some embodiments,operation 1620 may be omitted.

In an operation 1625, a cortical bone image is generated from thein-phase image. In some embodiments, the cortical bone image may beobtained as explained above by subtracting an in-phase image from anultra-short echo time image. In other embodiments when the imagingvolume is a pelvic area or other area where no cortical bone/airadjacencies are expected to exist, the cortical bone image may beobtained by inverting the in-phase image and registration with a boneprobability atlas.

In an operation 1630 the magnetic resonance data is segmented into a fatsegment, a water segment, a cortical bone segment, and an air segmentusing the images which were reconstructed in operations 1610 through1625. In some embodiments, the fat segment and the water segment may beobtained via a Dixon acquisition. In some embodiments, the air segmentmay be obtained by adding the in-phase image to the cortical bone imagegenerated according to operations set forth above.

In an operation 1635, a predetermined bulk density value for fat isassigned to the fat segment, a predetermined bulk density value forwater is assigned to the water segment, a predetermined bulk densityvalue for cortical bone is assigned to the cortical bone segment, and apredetermined bulk density value for air is assigned to the air segment.Then, the various segments with the corresponding assigned bulk densityvalues may be combined to produce a bulk density map for the imagingvolume. In some embodiments, the predetermined bulk density values maybe determined based on empirical data for a plurality of individuals. Insome embodiments, the predetermined bulk density values may bedetermined at least in part based on characteristics of an individualpatient, which may include the patient's age, sex, etc.

In an operation 1640, a bulk density map (i.e., an electron bulk densitymap) is created using the fat, water, cortical bone, and air segments.

In some embodiments, the bulk density map is created from the segmentsby: determining, for each of a plurality of voxels of the imagingvolume, which element among fat, water, cortical bone and air segment isprimarily represented in the voxel; and assigning a corresponding bulkdensity value to each voxel, where the assigned bulk density valuedepends on which element among fat, water, cortical bone and air isprimarily represented in the voxel.

In some embodiments, the bulk density map is created from the segmentsby: determining, for each of a plurality of voxels of the imagingvolume, a plurality of fractions which pertain to that voxel, includinga fat fraction, a water fraction, a cortical bone fraction, and an airfraction; and for each of the plurality of voxels, weighting each of theplurality of fractions by the corresponding bulk density value.

In an operation 1645, one or more digitally reconstructed radiographs(DRRs) are created using the electron bulk density map created inoperation 1520. In some embodiments, operation 1645 may be omitted.

In an operation 1650, one or more artificial computed tomography imagesare generated based on the fat, water, cortical bone, and air fractionsin each voxel. In some embodiments, operation 1650 may be omitted.

Although not illustrated in FIG. 16, in some embodiments the method mayfurther include an operation of transferring a bulk density map, one ormore DRRS, and/or one or more artificial computed tomography images to aradiation treatment planning system. In some embodiments, images may betransferred in accordance with the Digital Imaging and Communications inMedicine (DICOM) standard. In other embodiments, DRRs may be generatedby the treatment planning system, for example using the electron bulkdensity map.

FIG. 17 shows some example images which may be generated from magneticimage data for treatment planning. In particular, FIG. 17 illustratessome example images which may be generated in methods 1400, 1500 and/or1600 described above. FIG. 18 shows a Dixon in-phase image 1710, a bulkdensity map 1720, and an artificial computed tomography (CT) image 1730.

FIG. 18 shows yet another embodiment of a medical apparatus 1800.

Medical apparatus 1800 is similar to medical apparatus 1100 describedabove. However, medical apparatus 1800 includes in storage 1030 andmemory 1032 instructions, data, and software modules which allow it toexecute one or all of the methods 1400, 1500, and 1600. In particular,storage 1030 includes bulk density map generation commands 1850 forexecuting one or more of the methods 1400, 1500 and 1600, and memory1032 includes bulk density map generation command generation module1852.

Also, although not specifically illustrated in FIG. 18, in someembodiments storage 1030 may include a plurality of segments of themagnetic resonance data, including a fat segment, a water segment, acortical bone segment, and an air segment. Additionally, although notspecifically illustrated in FIG. 18, in some embodiments storage 1030may include a plurality of predetermined bulk density values to fat,water, cortical bone and air. Moreover, in some embodiments, althoughnot specifically illustrated in FIG. 18, storage 1030 may include one ormore automated computed tomography (CT) images. Furthermore, in someembodiments, storage 1030 may include a bone probability atlas.

Similarly, although not specifically illustrated in FIG. 18, in someembodiments memory 1032 may include an imaging volume segmentationmodule, a bulk density value assignment module, an automated computedtomography image generation module, and/or a bone probability atlasregistration module.

Accordingly, medical apparatus 1800 may be configured to execute one ormore of the methods 1400, 1500 and 1600 described above.

FIG. 19 illustrates an example embodiment of operations which may beperformed by a system and method which acquire magnetic resonance dataand process the magnetic resonance data for treatment planning. Inparticular, FIG. 19 illustrates: a magnetic resonance data acquisitionoperation 1910 which produces first and second echo images; a Dixonreconstruction operation 1920 which produces an in-phase image 1922, awater image 1924, and a fat image 1926; a tissue classification andelectron bulk density assignment operation 1930 which produces abone-enhanced image 1932 and an electron bulk density map 1934, and afiltering operation 1940 which filters bone-enhanced image 1932 andelectron bulk density map 1934 with a bone probability atlas 1936 toproduce a filtered bone-enhanced image 1942 and a filtered electron bulkdensity map 1944.

FIG. 20 shows an example embodiment of modules and corresponding workflow for a system and method which acquire magnetic resonance data andprocess the magnetic resonance data for treatment planning. Inparticular, FIG. 20 illustrates a magnetic resonance image andregistration module 2010, an automated segmentation and tissueclassification module 2020, an imaging/planning interface 2030, and asimulation and planning platform 2040. Magnetic resonance image andregistration module 2010 produces a bone image 2012 (e.g., from a T1weighted ultra-short time echo (UTE), water/fat images 2014 (e.g., byemploying a Dixon algorithm), a pathologic image 2016 (e.g., aT2-weighted image), and a functional MR image 2018 (e.g., a T2 image, adynamic contrast enhanced (DCE) image, a diffusion weighted image (DWI),etc.). Automated segmentation and tissue classification module 2020receives from images 2012, 2014, 2016 and 2018 and generates therefromsegments 2022, corresponding to bone, air and soft tissue (e.g., a watersegment and a fat segment), and one or more images 2024 of a tumor,target organ and risk strictures for treatment planning.Imaging/planning interface 2030 communicates or transfers a magneticresonance volume image 2032 (e.g., in DICOM format), an electron bulkdensity map and/or one or more automated computed tomography images(s)2034 (e.g., in DICOM format), and a tissue mask for autocontouring(e.g., in DICOM format). Simulation and planning platform 2040 receivesimages 2032, 2034 and 2036 and generates therefrom a treatment plan2042.

While the invention has been illustrated and described in detail in thedrawings and foregoing description, such illustration and descriptionare to be considered illustrative or exemplary and not restrictive; theinvention is not limited to the disclosed embodiments.

Other variations to the disclosed embodiments can be understood andeffected by those skilled in the art in practicing the claimedinvention, from a study of the drawings, the disclosure, and theappended claims. In the claims, the word “comprising” does not excludeother elements or steps, and the indefinite article “a” or “an” does notexclude a plurality. A single processor or other unit may fulfill thefunctions of several items recited in the claims. The mere fact thatcertain measures are recited in mutually different dependent claims doesnot indicate that a combination of these measured cannot be used toadvantage. A computer program may be stored/distributed on a suitablemedium, such as an optical storage medium or a solid-state mediumsupplied together with or as part of other hardware, but may also bedistributed in other forms, such as via the Internet or other wired orwireless telecommunication systems. Any reference signs in the claimsshould not be construed as limiting the scope.

LIST OF REFERENCE NUMERALS X

-   -   300 pulse sequence    -   302 RF    -   304 read out gradient    -   306 data acquisition gate    -   308 nuclear magnetic resonance signal    -   310 radio frequency pulse    -   312 time T_(RF)    -   314 free induction decay    -   316 first gradient echo    -   318 second gradient echo    -   320 first gradient pulse    -   322 second gradient pulse    -   324 third gradient pulse    -   326 TE₁    -   328 TE₂    -   330 TE₃    -   332 TAQ1    -   334 TAQ2    -   336 TAQ3    -   400 cortical bone image    -   402 cortical bone    -   500 fat-only (water-saturated) image    -   502 medullary bone    -   600 complete bone image    -   602 cortical plus medullary bone    -   700 fat-saturated image    -   800 in-phase image    -   900 ultra-short echo time image (phase)    -   902 air    -   1000 medical apparatus    -   1002 magnetic resonance imaging system    -   1004 magnet    -   1006 bore of magnet    -   1008 imaging zone    -   1010 magnetic field gradient coil    -   1012 magnetic field gradient coil power supply    -   1014 radio frequency coil    -   1016 transceiver    -   1018 subject    -   1020 subject support    -   1022 computer    -   1024 hardware interface    -   1026 processor    -   1028 user interface    -   1030 computer storage    -   1032 computer memory    -   1034 pulse sequence    -   1036 magnetic resonance data    -   1038 in-phase image    -   1040 fat-saturated image    -   1042 water-saturated image    -   1044 ultra-short echo time image    -   1046 opposed phase image    -   1048 medullary bone image    -   1050 cortical bone image    -   1052 complete bone image    -   1054 spatially dependent radiation attenuation coefficient    -   1056 radiation therapy planning data    -   1058 treatment plan    -   1060 control module    -   1062 image reconstruction module    -   1064 image manipulation module    -   1066 three-point Dixon signal model    -   1068 image segmentation module    -   1070 radiation attenuation coefficient calculation module    -   1072 radiation therapy planning data generation module    -   1074 graphical user interface control module    -   1076 graphical user interface    -   1078 radiation therapy planning interface    -   1122 radiation therapy system    -   1124 cryostat    -   1126 superconducting coil    -   1128 compensation coil    -   1130 reduced magnetic field region    -   1132 gantry    -   1133 axis of rotation    -   1134 radiotherapy source    -   1135 rotational actuator    -   1138 radiation beam    -   1140 support positioning system    -   1142 target zone    -   1150 radiation therapy control commands    -   1152 radiation therapy control command generation module    -   1200 medical apparatus    -   1202 radio-isotope imaging system    -   1204 scintillator ring    -   1206 light pipes    -   1208 light detectors    -   1210 concentration of radio isotope    -   1212 radiation    -   1220 radio-isotope imaging data    -   1222 medical image    -   1230 medical image reconstruction module    -   1240 digital reconstructed radiograph (DRR)    -   1710 Dixon in-phase image    -   1720 bulk density map    -   1730 artificial computed tomography image    -   1800 medical apparatus    -   1850 bulk density map generation commands    -   1852 bulk density map generation command generation module    -   1910 magnetic image acquisition operation    -   1920 Dixon reconstruction operation    -   1922 in-phase image    -   1924 water image    -   1926 fat image    -   1930 tissue classification and electron bulk density assignment        operation    -   1932 bone-enhanced image    -   1934 electron bulk density map    -   1936 bone probability map    -   1940 filtering operation    -   1942 filtered bone-enhanced image    -   1944 filtered electron bulk density map    -   2010 magnetic resonance imaging and registration operation    -   2012 cortical bone image    -   2014 water/fat image    -   2016 pathologic image    -   2018 functional magnetic resonance image    -   2020 automatic segmentation and classification operation    -   2022 bone, air, fat, water segmentation    -   2024 tissue, tumor, risk structure classification    -   2030 imaging and planning interface    -   2032 magnetic resonance volume    -   2034 bulk density mask    -   2036 tissue mask for autocontouring    -   2040 simulation and treatment planning platform    -   2042 treatment plan

What is claimed is:
 1. An apparatus, comprising: a magnetic resonanceimaging system which acquires magnetic resonance data from an imagingvolume; a processor for controlling the apparatus; and a memorycontaining machine executable instructions and a pulse sequence, whereinthe magnetic resonance data is acquired using the pulse sequenceincludes gradient echo data, wherein execution of the instructionscauses the processor to: acquire the magnetic resonance data using themagnetic resonance imaging system and the pulse sequence; and segmentthe magnetic resonance data into a plurality of segments, including afat segment, a water segment, a cortical bone segment, and an airsegment; and create a bulk density map of the imaging volume from thesegments.
 2. The apparatus of claim 1, wherein execution of theinstructions further causes the processor to create the bulk density mapfrom the segments by: determining for each of a plurality of voxels ofthe imaging volume, which element among fat, water, cortical bone andair segment is primarily represented in the voxel; and assigning acorresponding bulk density value to each voxel, where the assigned bulkdensity value depends on which element among fat, water, cortical boneand air is primarily represented in the voxel.
 3. The apparatus of claim1, wherein execution of the instructions further causes the processor tocreate the bulk density map from the segments by: assigningcorresponding bulk density values to fat, water, cortical bone and air;determining, for each of a plurality of voxels of the imaging volume, aplurality of fractions which pertain to the voxel, including a fatfraction, a water fraction, a cortical bone fraction, and an airfraction; and for each of the plurality of voxels, weighting each of theplurality of fractions by the corresponding bulk density value.
 4. Theapparatus of claim 1, wherein execution of the instructions furthercauses the processor to generate one or more digitally reconstructedradiographs (DRRs) from the magnetic resonance data.
 5. The apparatus ofclaim 4, wherein execution of the instructions further causes theprocessor to transfer the one or more DRRs to a radiation treatmentplanning system.
 6. The apparatus of claim 1, wherein execution of theinstructions further causes the processor to generate an artificialcomputed tomography image based on fractions of fat, water, air, andcortical bone in each voxel of the imaging volume.
 7. The apparatus ofclaim 1, wherein execution of the instructions further causes theprocessor to reconstruct an in-phase image, a fat-saturated image, awater-saturated image, and an ultra-short echo time image from themagnetic resonance data, and to produce the cortical bone segment bysubtracting a scaled multiple of the in-phase image from the ultra-shortecho time image.
 8. The apparatus of claim 1, wherein execution of theinstructions further causes the processor to reconstruct an in-phaseimage, a fat-saturated image, and a water-saturated image from themagnetic resonance data, and to produce the cortical bone segment byautomatically thresholding a noise level in the in-phase image andsubsequently removing background noise.
 9. The apparatus of claim 8,wherein execution of the instructions further causes the processor toproduce the cortical bone segment by registering the in-phase image witha bone probability atlas.
 10. The apparatus of claim 1, whereinexecution of the instructions further causes the processor to transferthe bulk density map to a radiation treatment planning system.
 11. Amethod, comprising: acquiring magnetic resonance data from an imagingvolume via a magnetic resonance imaging system and a pulse sequence,wherein the magnetic resonance data includes gradient echo data;segmenting the magnetic resonance data into a plurality of segments, thesegments including a fat segment, a water segment, a cortical bonesegment, and an air segment; and creating a bulk density map of theimaging volume from the segments.
 12. The method of claim 11, whereincreating the bulk density map from the segments comprises: determining,for each of a plurality of voxels of the imaging volume, which elementamong fat, water, air and cortical bone is primarily represented in thevoxel; and assigning a corresponding bulk density value to each voxel,where the assigned bulk density value depends on which element amongfat, water, cortical bone, and air is primarily represented in thevoxel.
 13. The method of claim 11, wherein creating the bulk density mapfrom the segments comprises: assigning corresponding bulk density valuesto fat, water, cortical bone and air; determining, for each of aplurality of voxels of the imaging volume, a plurality of fractionswhich pertain to the voxel, including an a fat fraction, a waterfraction, a cortical bone fraction and an air fraction; and for each ofthe plurality of voxels, weighting each of the plurality of fractions bythe corresponding bulk density value.
 14. The method of claim 11,further comprising generating one or more digitally reconstructedradiographs (DRRs) from the magnetic resonance data.
 15. The method ofclaim 14, further comprising transferring the one or more DRRs to aradiation treatment planning system.
 16. The method of claim 11, furthercomprising generating an artificial computed tomography image based onfractions of fat, water, cortical bone, and air in each voxel of theimaging volume.
 17. The method of claim 11, further comprising:reconstructing an in-phase image, a fat-saturated image, awater-saturated image, and an ultra-short echo time image from themagnetic resonance data; and producing the cortical bone segment bysubtracting a scaled multiple of the in-phase image from the ultra-shortecho time image.
 18. The method of claim 11, further comprising:reconstructing an in-phase image, a fat-saturated image, and awater-saturated image from the magnetic resonance data; and producingthe cortical bone segment by automatically thresholding a noise level inthe in-phase image and subsequently removing background noise.
 19. Themethod of claim 18, wherein producing the cortical bone segment furthercomprises registering the in-phase image with a bone probability atlas.20. A non-transitory computer-readable storage medium having storedtherein a pulse sequence and machine readable instructions configured tobe executed by a processor to control an apparatus including a magneticresonance imaging system, the machine readable instructions beingconfigured in conjunction with the pulse sequence to cause the apparatusto execute a process comprising: acquiring magnetic resonance data froman imaging volume using the magnetic resonance imaging system and thepulse sequence, wherein the magnetic resonance data includes gradientecho data; segmenting the magnetic resonance data into a plurality ofsegments, the segments including a fat segment, a water segment, acortical bone segment, and an air segment; and creating a bulk densitymap of the imaging volume from the segments.